[BioC] microarray outlier detection
guest [guest]
guest at bioconductor.org
Fri Aug 30 22:32:33 CEST 2013
Dear users,
I have human gene 2.0 st array, total 12 samples including 4 groups, each group has 3 replicates. The lab person would like to remove one from each of the group due to the outliers, but from PCA plot, the samples are not clustered, it is hard to remove any sample as an outlier. I wonder if we have the package or function to solve the outlier detection issue on microarray.
Thanks,
-- output of sessionInfo():
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] pd.hugene.2.0.st_3.8.0 oligo_1.24.1 oligoClasses_1.22.0 hugene20sttranscriptcluster.db_2.12.1
[5] org.Hs.eg.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6
[9] Biobase_2.20.1 BiocGenerics_0.6.0 limma_3.16.6
loaded via a namespace (and not attached):
[1] affxparser_1.32.3 affyio_1.28.0 BiocInstaller_1.10.3 Biostrings_2.28.0 bit_1.1-10 codetools_0.2-8
[7] ff_2.2-11 foreach_1.4.1 GenomicRanges_1.12.4 IRanges_1.18.2 iterators_1.0.6 preprocessCore_1.22.0
[13] splines_3.0.1 stats4_3.0.1 zlibbioc_1.6.0
--
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